diff TextExporter.xml @ 11:1c596fdaf34a draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"

--- a/TextExporter.xml	Thu Sep 24 12:32:20 2020 +0000
+++ b/TextExporter.xml	Tue Oct 13 20:09:21 2020 +0000
@@ -18,9 +18,7 @@
 ## Preprocessing
 mkdir in &&
 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
-#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  mkdir out &&
-#end if
+mkdir out &&
 #if "centroids_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir consensus_centroids &&
 #end if
@@ -39,10 +37,8 @@
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
-#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  -out
-  'out/output.${gxy2omsext("csv")}'
-#end if
+-out
+'out/output.${gxy2omsext("tabular")}'
 #if "centroids_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -consensus:centroids
   'consensus_centroids/output.${gxy2omsext("csv")}'
@@ -60,9 +56,7 @@
 #end if
 
 ## Postprocessing
-#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
-  && mv 'out/output.${gxy2omsext("csv")}' '$out'
-#end if
+&& mv 'out/output.${gxy2omsext("tabular")}' '$out'
 #if "centroids_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   && mv 'consensus_centroids/output.${gxy2omsext("csv")}' '$consensus_centroids'
 #end if
@@ -122,23 +116,20 @@
       <param name="sort_by_size" argument="-consensus:sort_by_size" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply a stable sort by decreasing size" help="(i.e., the number of elements)"/>
     </section>
     <expand macro="adv_opts_macro">
-      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
+      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
       <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
         <expand macro="list_string_san"/>
       </param>
     </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false">
-      <option value="out_FLAG">out (Apply a stable sort by decreasing size)</option>
-      <option value="centroids_FLAG">centroids (Apply a stable sort by decreasing size)</option>
-      <option value="elements_FLAG">elements (Apply a stable sort by decreasing size)</option>
-      <option value="features_FLAG">features (Apply a stable sort by decreasing size)</option>
+    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
+      <option value="centroids_FLAG">centroids (Output file for centroids of consensus features)</option>
+      <option value="elements_FLAG">elements (Output file for elements of consensus features)</option>
+      <option value="features_FLAG">features (Output file for consensus features and contained elements from all maps (writes 'nan's if elements are missing))</option>
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
   <outputs>
-    <data name="out" label="${tool.name} on ${on_string}: out" format="csv">
-      <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
-    </data>
+    <data name="out" label="${tool.name} on ${on_string}: out" format="tabular"/>
     <data name="consensus_centroids" label="${tool.name} on ${on_string}: consensus:centroids" format="csv">
       <filter>OPTIONAL_OUTPUTS is not None and "centroids_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
@@ -148,9 +139,6 @@
     <data name="consensus_features" label="${tool.name} on ${on_string}: consensus:features" format="csv">
       <filter>OPTIONAL_OUTPUTS is not None and "features_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
-    <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
-      <filter>OPTIONAL_OUTPUTS is None</filter>
-    </data>
     <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
@@ -162,6 +150,6 @@
   <help><![CDATA[Exports various XML formats to a text file.
 
 
-For more information, visit http://www.openms.de/documentation/TOPP_TextExporter.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_TextExporter.html]]></help>
   <expand macro="references"/>
 </tool>